added homova command

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index d46cf740bd744697cc5caccdd2724d31edca6bac..c0b9aec10e4f8695f040e61e80910a8efeb310af 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -324,7 +324,7 @@ void AmovaCommand::help(){
                m->mothurOut("The amova command parameters are phylip, iters, groups, label, design, sets and processors.  The design parameter is required.\n");
                m->mothurOut("The design parameter allows you to assign your groups to sets when you are running amova. It is required. \n");
                m->mothurOut("The design file looks like the group file.  It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n");
-               m->mothurOut("The sets parameter allows you to specify which of the sets in your designfile you would like to analyze. The set names are separated by dashes. THe default is all sets in the designfile.\n");
+               m->mothurOut("The sets parameter allows you to specify which of the sets in your designfile you would like to analyze. The set names are separated by dashes. THe default is all sets in the designfile. To run the pairwise comparisons of all sets use sets=all.\n");
                m->mothurOut("The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n");
                m->mothurOut("The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes. groups=all will find all pairwise comparisons. \n");
                m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");